When you leave from a village and go too far , stay in a place a while and then return to the village , all villagers disappear. This also happens when spawning a villager with an egg. It seems that when the game unloads the chink where villagers are and the loads it again it deletes villagers. The only way to never loose the villagers is by staying in or near the village always.
It seems it's more likely to happen when you edit their houses.